[pymvpa] shogun 6.6/pymvpa bug

[Scott Gorlin]

Hi,

I just upgraded my system, and after reinstalling some packages, noticed 
a few bugs.  Pymvpa does not seem to work with the latest release of 
Shogun 0.6.6.

Running clfs_examples gives the following output then error:

Dummy 2-class univariate with 2 useful features out of 100
 Dataset / float64 60 x 100
uniq: 2 labels 6 chunks labels_mapped
stats: mean=0.00195773 std=0.213342 var=0.0455148 min=-0.752662 max=1
Counts of labels in each chunk:
  chunks\labels  0   1
                --- ---
       0         5   5
       1         5   5
       2         5   5
       3         5   5
       4         5   5
       5         5   5

Original labels were mapped using following mapping:
    L0:    0
    L1:    1

Summary per label across chunks
  label mean std min max #chunks
   0      5   0   5   5     6
   1      5   0   5   5     6

Summary per chunk across labels
  chunk mean std min max #labels
   0      5   0   5   5     2
   1      5   0   5   5     2
   2      5   0   5   5     2
   3      5   0   5   5     2
   4      5   0   5   5     2
   5      5   0   5   5     2

 Classifier                                  %corr  #features     train 
predict  full
  SMLR(lm=0.1)                            :   85.0%   22       0.07s  
0.00s   0.43s
  SMLR(lm=1.0)                            :   91.7%   10       0.00s  
0.00s   0.04s
  Pairs+maxvote multiclass on SMLR(lm=0.1):   85.0%   100      0.08s  
0.00s   0.48s
  libsvm.LinSVM(C=def)                    :   78.3%   100      0.01s  
0.00s   0.10s
  libsvm.LinSVM(C=10*def)                 :   81.7%   100      0.01s  
0.00s   0.11s
  libsvm.LinSVM(C=1)                      :   81.7%   100      0.01s  
0.00s   0.11s
  libsvm.LinNuSVM(nu=def)                 :   78.3%   100      0.01s  
0.00s   0.11s
  libsvm.RbfSVM()                         :   75.0%   100      0.01s  
0.00s   0.08s
  libsvm.RbfNuSVM(nu=def)                 :   78.3%   100      0.01s  
0.00s   0.08s
  libsvm.PolySVM()                        :   75.0%   100      0.01s  
0.00s   0.10s
  sg.LinSVM(C=def)/libsvm                 :
Traceback (most recent call last):
  File "clfs_examples.py", line 90, in <module>
    main()
  File "clfs_examples.py", line 71, in main
    clf.train(training_ds)
  File "/usr/lib/python2.5/site-packages/mvpa/clfs/base.py", line 375, 
in train
    result = self._train(dataset)
  File "/usr/lib/python2.5/site-packages/mvpa/clfs/sg/svm.py", line 287, 
in _train
    *kargs)
  File "/usr/local/lib/python2.5/site-packages/shogun/Kernel.py", line 
1303, in __init__
    this = _Kernel.new_LinearKernel(*args)
NotImplementedError: Wrong number of arguments for overloaded function 
'new_LinearKernel'.
  Possible C/C++ prototypes are:
    CLinearKernel()
    CLinearKernel(CRealFeatures *,CRealFeatures *)


I placed the crossvalidation step in a try block, and noticed that most 
of the shogun classes in clfs_examples failed.  The exceptions (which 
did work) called sg.SomeClass() without any arguments, leading me to 
believe there is some weird API change in shogun.  All of the examples 
in Shogun's python-modular tests work just fine.

After I reinstalled Shogun 0.6.4, everything worked fine.  Then I 
reinstalled 0.6.6, and it didn't work again.

I am running Ubuntu 8.10 in python 2.5 with pymvpa 0.3.1.

Thanks!
Scott